Polymerase chain reaction (PCR) and other detection systems rely upon the accurate and consistent positioning of sample well plates, and other carriers or supports, to perform accurate measurements of sample fluorescence in arrays of sample wells. When the 96 or other number of sample wells in a standard microtitre plate, or other plate configuration, are not accurately aligned with the read path of the optical detector, the peak signal intensities associated with individual wells can be incorrectly measured and recorded. Systems employing spectral filters on the detection optics can likewise experience spectral shifts when the filter optics are skewed from desired alignments. Other detection artifacts can occur when the detection or imaging optics are not accurately aligned with the sample wells, or other detection regions. Correct detection and alignment of the optical reader with the sample wells is a significant objective for these and other detection systems.